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Charles Plessy

The Center for Integrative Medical Sciences (IMS) is calling for applicants to its program:

The IMS applies interdisciplinary approaches which includes genome-wide medical science, immunology and physiology, bioinformatics, and molecular, biochemical and quantitative sciences.

Applicants must be distinguished international students in a Master's or Ph.D. course or young postdocs who received their Ph.D. within the last three years.

Open data has a source; this week's Policy Forum in Science reminds to respect it:

“researchers using open data should strive to conduct ethical studies relevant to local communities and return results to them”

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Sequencing genes by studying the population of !

Published in Nature Genetics today by Jagadeesan, ..., and Helgason from Genetics and the University of Iceland.

The application deadline for the - Institute Joint Doctoral Course has been extended!

All interested in participating can apply till The, Feb 1st, 2018.

RIKEN CLST will be able to fund part of the travel costs for a limited number of students from Japanese Universities.

For more details and the registration page please consult the below link.

I will teach about research at the course "Bioinformatics analysis of gene regulation in omics data and its applications to medical problems" organised by the Institute ( Course number 3027) and . The course will take place in from March 5 to March 9. Course websites: <, <

Perhaps we should supplement the singular and plural forms with a dual form ( in scientific litterature to make it clearer when "multiple" means "only two".

Extracting factual information from abstracts of high-impact journals is a cognitive challenge. For instance, beginners may not pay attention that claims such as "in diverse cell types" may only mean "in the two cell types that we tested". This reminds me a bit the patent jargon...

Complex microreactors carrying chemical reactions between between reagents brought by individual were assembled by Wang, ..., and Grzybowski (Ulsan, South ).

New surfactants containing gold, iron oxide or lead sulfide were used to create droplets that aggregate in magnetic fields, translate or rotate under laser illumination, and weld together electric fields. Published in .

Toxic adapted to feed from our food ...

A study published in by Collins, ..., and Britton, from the Baylor College of Medicine, suggests that a subpopulation of gut bacteria adapted to the presence of in our intestines, where it can be found in larger amounts since 2000/2001 when this additive was approved in the US and the EU. Article: Free summary:

Cells induced to differentiate and colonise a target organ: In this week's issue of , by Han, ..., and Lerner from The Scripps, who found a single synthethic gene sending cells to the brain.

In brief: a library of single-chain antibodies was transfected in bone-marrow cells, which were translanted in mice. The cells that migrated in the brain were enriched for a synthethic gene expresing an that binds Vimentin and causes it to be phosphorylated.

The Journal of Neuroscience has just launched a mentoring program for new reviewers, who will train themselves on manuscripts submitted to .

In the R language, given tables in matrix, data.frame or data.table classe, I did not find a safe way to extract a column whose position is given by a variable. The multi-element operator pattern [, i] will not work out of the box in data.table, which expects [,i,with=F] instead, and the single-element operator pattern [[i]] will not work with matrices, which will return their ith element. Is there another operator that will extract safely a column over multiple classes of tables ?

Just realised that since R 3.4.0, the debugonce function has a signature argument to handle S4 methods. Very useful ! Now I wonder if there is a signature expression that can be used to mean "whichever signature is good, please just match my next function call".

Use bioSyntax ( to color files containing biological data in various formats (SAM, BED, ALN, FASTQ, etc.). Source:

An entirely factor was developped by Erwin, Ansari (+others) at the University of Wisconsin-Madison (+elsewhere).

It binds DNA through a pyrrole- and imidazole-based polyamide specific for the sequence AAGAAGAAG, which is dramatically expanded in the genome of Friedreich's ataxia's patients.

Its other half is a drug (JQ1) that recruits the transcription elongation factor BRD4, which rescues expression of the mutated gene.

Very impressive. is a nice website to help us do exacty what its name suggests. After answering a bunch of questions to the website, it returns a list of suggested actions, such as enabling two-factor authorization, using a password manager, etc.

Note for self: volume of .

Calculated with R's () "units" package (<

drop_volume <- function(Diameter, Unit) {
Diameter <- set_units(Diameter, "μm")
Volume <- 4/3*pi*(Diameter/2)^3
set_units(Volume, Unit)

drop_volume(1, "fL")
# 0.5235988 fL

drop_volume(10, "pL")
# 0.5235988 pL

drop_volume(100, "nL")
# 0.5235988 nL